Contacts of the strand formed by residues 283 - 288 (chain C) in PDB entry 1D2H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C GLY* 4.6 2.0 - - - -
138C ASN* 4.0 22.0 - - + +
173C ASP* 4.4 14.8 - - - -
174C HIS 4.0 2.5 - - - -
175C LYS* 2.8 48.2 + - + -
176C ASN* 4.4 0.2 - - - +
190C LYS* 4.3 4.9 - - + -
191C ASN* 4.1 35.9 + - - +
192C ILE* 3.9 30.5 - - + -
193C TYR* 4.2 16.7 - + - -
268C GLY 2.5 19.8 + - - +
269C ASP* 2.9 24.7 + - - +
282C CYS* 1.3 88.1 - - + +
284C PHE* 1.3 61.4 + - - +
285C ILE* 3.4 4.5 - - + +
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Residues in contact with PHE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ASP* 3.0 22.9 - - - +
174C HIS* 3.0 49.6 + - + +
176C ASN* 3.6 36.8 - - + -
178C ASP* 4.1 9.2 - - - -
247C LEU* 3.3 30.3 - - + -
266C VAL* 3.5 21.8 - - + -
267C LEU 3.9 1.1 - - - -
268C GLY 3.3 8.5 - - - -
273C TYR* 3.7 41.1 - + - -
281C PRO* 3.8 13.7 - - + -
283C TYR* 1.3 72.0 - - - +
285C ILE* 1.3 59.4 + - - +
286C HIS* 4.1 2.3 - - - +
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Residues in contact with ILE 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C TRP* 4.2 13.5 - - + -
136C LEU* 4.9 1.3 - - + -
171C VAL* 3.7 27.6 - - + -
173C ASP* 4.0 12.6 - - + +
193C TYR* 3.7 16.6 - - + +
265C SER 3.3 1.9 - - - +
266C VAL* 3.0 4.8 - - - +
267C LEU* 3.0 41.9 + - + +
269C ASP 3.0 24.5 - - - +
270C PHE* 3.6 33.2 - - + -
283C TYR* 3.4 7.0 - - + +
284C PHE* 1.3 76.5 - - - +
286C HIS* 1.3 65.3 + - - +
287C VAL* 3.7 1.4 + - + +
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Residues in contact with HIS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LEU 2.9 13.9 - - - +
171C VAL* 3.4 3.0 - - - -
172C ILE* 2.9 37.0 + - + +
174C HIS* 3.5 15.8 - + - -
247C LEU* 3.3 20.5 - - + +
250C PHE* 3.7 19.4 - + + -
251C THR* 3.4 39.5 - - - -
254C VAL* 3.8 5.4 - - + +
264C HIS* 3.2 23.4 - + + +
265C SER 3.2 5.2 - - - +
266C VAL* 3.6 12.4 - - + +
284C PHE 4.4 1.3 - - - -
285C ILE* 1.3 79.8 - - - +
287C VAL* 1.3 59.9 + - - +
288C LEU* 4.8 8.7 - - + +
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C TRP* 5.1 7.6 - - + -
51C LEU* 3.9 39.7 - - + -
55C HIS* 6.2 0.7 - - + -
169C LEU* 4.5 10.3 - - + -
170C LEU 3.2 5.8 - - - +
171C VAL* 4.7 8.7 - - + +
263C GLN 3.5 2.5 - - - +
264C HIS* 3.5 1.2 - - - -
265C SER* 2.8 58.6 + - - +
267C LEU* 5.1 6.3 - - + -
285C ILE* 3.7 3.3 + - + +
286C HIS* 1.3 72.6 - - - +
288C LEU* 1.3 67.8 + - - +
289C LYS* 4.3 0.7 - - + -
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C VAL* 5.2 0.2 - - - +
168C GLY 2.8 1.7 - - - +
169C LEU* 2.6 39.4 + - - -
170C LEU* 2.9 32.3 + - + +
254C VAL* 3.4 39.5 - - + +
255C GLN* 5.2 0.4 - - + -
258C PHE* 3.5 29.8 - - + -
262C CYS* 4.3 8.5 - - + -
263C GLN 3.8 1.6 - - - +
264C HIS* 3.1 47.6 - - + +
286C HIS* 4.8 6.3 - - + -
287C VAL* 1.3 76.5 - - - +
289C LYS* 1.3 56.1 + - - +
290C LYS 3.5 1.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il